The name can be confusing because it does sound like there would be some sort of z-index ordering or something. However, layers' only job is to determine whether or not a shape gets rendered. If a layer rule returns true, the shapes in that layer will be visible. If a layer rule returns false, the shapes in that layer will not be rendered. That's all there is to it.
This is really useful for authenticated/non-authenticated scenarios. Also, since the layer rules are extensible, you can add your own complex scenarios. Say for example, you want to have widgets on your site during work hours only. You could build your own layer rule extension and create a layer for widgets called "office-hours-only".